Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	Gene Summary
	Phenotypic Information (metabolism pathway, cancer, disease, phenome)
	Mutations : SVs, CNVs, SNVs
	Gene expression: GE, Protein, DEGE, CNV vs GE
	Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG
	Pharmacological Information: Drug-Gene Network
	Cross referenced IDs

Gene Summary for MGAM

Basic gene info.	Gene symbol	MGAM
	Gene name	maltase-glucoamylase (alpha-glucosidase)
	Synonyms	MG\|MGA
	Cytomap	UCSC genome browser: 7q34
	Genomic location	chr7 :141695678-141806547
	Type of gene	protein-coding
	RefGenes	NM_004668.2,
	Ensembl id	ENSG00000259858
	Description	brush border hydrolasemaltase-glucoamylase, intestinal
	Modification date	20141211
dbXrefs	MIM : 154360
	HGNC : HGNC
	Ensembl : ENSG00000257335
	HPRD : 01104
	Vega : OTTHUMG00000158395
Protein	UniProt: O43451 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MGAM
	BioGPS: 8972
	Gene Expression Atlas: ENSG00000259858
	The Human Protein Atlas: ENSG00000259858
Pathway	NCI Pathway Interaction Database: MGAM
	KEGG: MGAM
	REACTOME: MGAM
	ConsensusPathDB
	Pathway Commons: MGAM
Metabolism	MetaCyc: MGAM
	HUMANCyc: MGAM
Regulation	Ensembl's Regulation: ENSG00000259858
	miRBase: chr7 :141,695,678-141,806,547
	TargetScan: NM_004668
	cisRED: ENSG00000259858
Context	iHOP: MGAM
	cancer metabolism search in PubMed: MGAM
	UCL Cancer Institute: MGAM
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of MGAM in cancer cell metabolism	1. Yang S (2007) Gene amplifications at chromosome 7 of the human gastric cancer genome. International journal of molecular medicine 20: 225-231. go to article

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Phenotypic Information for MGAM(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MGAM
	Familial Cancer Database: MGAM

* This gene is included in those cancer gene databases.


Oncogene ¹	Tumor Suppressor gene ²	Cancer Gene Census ³	CancerGenes ⁴	Network of Cancer Gene ⁵	Significant driver gene in	Therapeutic Vulnerabilities in Cancer¹

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_GALACTOSE_METABOLISM KEGG_STARCH_AND_SUCROSE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM	154360; gene.
Orphanet
Disease	KEGG Disease: MGAM
	MedGen: MGAM (Human Medical Genetics with Condition)
	ClinVar: MGAM
Phenotype	MGI: MGAM (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MGAM

Mutations for MGAM

* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_b

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MGAM related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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SNV Counts per Each Loci in COSMIC data : go to COSMIC point mutation

: Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=7

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=37)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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Top 10 SNVs Having the Most Samples in COSMIC data

* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.

GRCh37 position	Mutation(aa)	Unique sampleID count
chr7:141708471-141708471	p.R98Q	7
chr7:141719069-141719069	p.S133F	4
chr7:141719073-141719073	p.K134N	2
chr7:141724852-141724852	p.N295N	2
chr7:141724853-141724853	p.G296R	2
chr7:141724872-141724872	p.A302V	2
chr7:141708362-141708362	p.P62S	2
chr7:141705382-141705382	p.V18F	2
chr7:141719039-141719039	p.G123E	2
chr7:141722220-141722220	p.R288K	2

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=5

Point Mutation/ Tissue ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	4	12	3	29	7		16		6	3		45	12	6		4	89	15	2	25
# mutation	4	12	3	36	6		17		5	3		51	13	6		4	160	18	2	44
nonsynonymous SNV	4	8	2	25	5		14		2	2		41	6	5		1	119	10	1	30
synonymous SNV		4	1	11	1		3		3	1		10	7	1		3	41	8	1	14

cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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Top 10 SNVs Having the Most Samples in TCGA data

* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.

Genomic Position	Mutation(aa)	Unique sampleID count
chr7:141758086	p.I1259I	5
chr7:141747587	p.R834Q	5
chr7:141759688	p.P1327P	5
chr7:141708471	p.R1097C	4
chr7:141754683	p.R98Q	4
chr7:141747669	p.P1359S	3
chr7:141797419	p.F1677F	3
chr7:141803141	p.T861T	3
chr7:141760126	p.E1800K	3
chr7:141719073	p.E976A	2

Other DBs for Point Mutations

Point Mutation Table of Ensembl: go to Ensembl variation table

Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

Copy Number for MGAM in TCGA

* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.

cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for MGAM

Gene Expression in Cancer Cell-lines (CCLE)

* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

Differential Gene Expression in Primary Tumors (TCGA)

* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))

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CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

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Gene-Gene Network Information

Co-Expressed gene's network Plot

* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types


AHCYL2,ATP12A,ATP1A4,BMPER,CASQ1,EGF,ESRRG, FRAS1,HERC1,ESRG,IGFBP2,LOC100128164,LOC374491,LRTM1, MGAM,MYNN,PPP1R3C,TMC3,TMPRSS7,WDR72,ZNF37BP	ADAM8,APOC1,CELA1,CHIT1,DEC1,DNAJC5B,HOXB9, HS3ST2,HTRA4,LILRA4,MGAM,LINC00112,NKX2-6,OR11A1, PKD2L1,PRAMEF22,SCARNA11,SDS,SNORA27,SULT1E1,TNFRSF11B

AJAP1,ARG1,AVPR1A,CLEC4D,COL15A1,CXCR1,CXCR2, SUPT20HL2,FPR1,FPR2,GPR97,HRH2,IL7R,LINGO4, MGAM,PADI4,PGLYRP1,S100A12,SELE,TCTE1,TNC	AADAC,ALDOB,APOA1,APOA4,APOB,APOC3,C17orf78, ERICH4,CEACAM20,CRISP1,DPEP1,ENPEP,FABP6,GSTA2, GSTA5,KCNJ13,LOC285733,MGAM,ONECUT3,SLC2A2,SLC5A12, SL

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for MGAM

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	O43451; -.
Chemistry	ChEMBL	CHEMBL2074; -.
Chemistry	GuidetoPHARMACOLOGY	2627; -.
Organism-specific databases	PharmGKB	PA30778; -.
Organism-specific databases	CTD	8972; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00284	maltase-glucoamylase (alpha-glucosidase)	approved; investigational	Acarbose
DB00491	maltase-glucoamylase (alpha-glucosidase)	approved	Miglitol
DB04878	maltase-glucoamylase (alpha-glucosidase)	approved; investigational	Voglibose
DB04465	maltase-glucoamylase (alpha-glucosidase)	experimental	Lactose

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Cross referenced IDs for MGAM

* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information